From 8b4c5742c93ae0a5e6f519adea58290ee720a97b Mon Sep 17 00:00:00 2001
From: Subazini TK <subazinitk@gmail.com>
Date: Fri, 13 May 2022 15:40:50 +0200
Subject: [PATCH] Update main.nf

---
 modules/hmtnote/main.nf | 23 +----------------------
 1 file changed, 1 insertion(+), 22 deletions(-)

diff --git a/modules/hmtnote/main.nf b/modules/hmtnote/main.nf
index 2025f5b7..bf9a155d 100644
--- a/modules/hmtnote/main.nf
+++ b/modules/hmtnote/main.nf
@@ -2,28 +2,15 @@ process HMTNOTE {
     tag "$meta.id"
     label 'process_low'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
         'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(vcf)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*_annotated.vcf"), emit: vcf
-    // TODO nf-core: List additional required output channels/values here
     path "versions.yml"           , emit: versions
 
     when:
@@ -32,15 +19,7 @@ process HMTNOTE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+
     """
     hmtnote \\
         annotate \\